Bulk RNA-sequencing (whole transcriptome) - Revision history

Michiel Perneel at 13:24, 24 September 2026

2026-09-24T13:24:39Z

← Older revision		Revision as of 06:24, 24 September 2026
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	The method is sensitive to how the sample is handled. Prokaryotic mRNA has a half-life of roughly 5 minutes, and as little as ~2.4 minutes in marine cyanobacteria.<ref name="Moran2013">Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., & Hopkinson, B. M. (2013). Sizing up metatranscriptomics. ''The ISME Journal'', 7(2), 237–243. doi:10.1038/ismej.2012.94</ref>		The method is sensitive to how the sample is handled. Prokaryotic mRNA has a half-life of roughly 5 minutes, and as little as ~2.4 minutes in marine cyanobacteria.<ref name="Moran2013">Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., & Hopkinson, B. M. (2013). Sizing up metatranscriptomics. ''The ISME Journal'', 7(2), 237–243. doi:10.1038/ismej.2012.94</ref>
	Protocol choices at every step during the generation of bulk RNA-Seq data such as filtration, preservation, enrichment (e.g. for mRNA in poly(A) selection to target microeukaryotic material), sequencing depth, assembly and annotation, affect the final expression matrix<ref name="Cohen2022">Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K., & Lampe, R. H. (2022). Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. ''Frontiers in Marine Science'', 9, 867007. doi:10.3389/fmars.2022.867007</ref>		Protocol choices at every step during the generation of bulk RNA-Seq data such as filtration, preservation, enrichment (e.g. for mRNA in poly(A) selection to target microeukaryotic material), sequencing depth, assembly and annotation, affect the final expression matrix<ref name="Cohen2022">Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K., & Lampe, R. H. (2022). Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. ''Frontiers in Marine Science'', 9, 867007. doi:10.3389/fmars.2022.867007</ref>

	~~== Specific use cases ==~~


	=== Sample collection and filtration ===		=== Sample collection and filtration ===
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	* Converting expression into a flux requires independent calibration (rate measurements, physiological data, or a model).		* Converting expression into a flux requires independent calibration (rate measurements, physiological data, or a model).

			== Specific use cases ==
			=== Viruses ===
			=== Life cycles ===
	== Example studies ==		== Example studies ==
	https://doi.org/10.1073/pnas.0708897105		https://doi.org/10.1073/pnas.0708897105

Michiel Perneel at 13:00, 24 September 2026

2026-09-24T13:00:14Z

← Older revision		Revision as of 06:00, 24 September 2026
Line 32:		Line 32:
	The method is sensitive to how the sample is handled. Prokaryotic mRNA has a half-life of roughly 5 minutes, and as little as ~2.4 minutes in marine cyanobacteria.<ref name="Moran2013">Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., & Hopkinson, B. M. (2013). Sizing up metatranscriptomics. ''The ISME Journal'', 7(2), 237–243. doi:10.1038/ismej.2012.94</ref>		The method is sensitive to how the sample is handled. Prokaryotic mRNA has a half-life of roughly 5 minutes, and as little as ~2.4 minutes in marine cyanobacteria.<ref name="Moran2013">Moran, M. A., Satinsky, B., Gifford, S. M., Luo, H., Rivers, A., Chan, L.-K., Meng, J., Durham, B. P., Shen, C., Varaljay, V. A., Smith, C. B., Yager, P. L., & Hopkinson, B. M. (2013). Sizing up metatranscriptomics. ''The ISME Journal'', 7(2), 237–243. doi:10.1038/ismej.2012.94</ref>
	Protocol choices at every step during the generation of bulk RNA-Seq data such as filtration, preservation, enrichment (e.g. for mRNA in poly(A) selection to target microeukaryotic material), sequencing depth, assembly and annotation, affect the final expression matrix<ref name="Cohen2022">Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K., & Lampe, R. H. (2022). Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. ''Frontiers in Marine Science'', 9, 867007. doi:10.3389/fmars.2022.867007</ref>		Protocol choices at every step during the generation of bulk RNA-Seq data such as filtration, preservation, enrichment (e.g. for mRNA in poly(A) selection to target microeukaryotic material), sequencing depth, assembly and annotation, affect the final expression matrix<ref name="Cohen2022">Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K., & Lampe, R. H. (2022). Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. ''Frontiers in Marine Science'', 9, 867007. doi:10.3389/fmars.2022.867007</ref>

			== Specific use cases ==


	=== Sample collection and filtration ===		=== Sample collection and filtration ===

Michiel Perneel: first draft of the Wiki, mainly based on Cohen et al., (2022)

2026-08-27T14:39:20Z

first draft of the Wiki, mainly based on Cohen et al., (2022)

Show changes

Michiel Perneel: Created page with "* Page authors: Michiel Perneel, PRIMO * Responsible curator: Kate Evans ---- TOC
{| class="model-ib" High-throughput sequencing of RNA transcribed by an individual or population of a given organism, or a community of species. |- | '''Approach:''' filtering, RNA extraction, sequencing, bioinformatics |- | '''Context:''' ''in situ'', culturing, incubations |- | '''Spatial s..."

2026-02-21T10:24:04Z

Created page with "* Page authors: Michiel Perneel, PRIMO * Responsible curator: Kate Evans ---- __TOC__ <div class="model-box"> {| class="model-ib" High-throughput sequencing of RNA transcribed by an individual or population of a given organism, or a community of species. |- | '''Approach:''' filtering, RNA extraction, sequencing, bioinformatics |- | '''Context:''' ''in situ'', culturing, incubations |- | '''Spatial s..."

New page

* [[Page authors|Page authors]]: [[Michiel Perneel]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Kate Evans|Kate Evans]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
High-throughput sequencing of RNA transcribed by an individual or population of a given organism, or a community of species.
|-
| '''Approach:''' filtering, RNA extraction, sequencing, bioinformatics
|-
| '''Context:''' ''in situ'', culturing, incubations
|-
| '''Spatial scale:''' L
|-
| '''Temporal scale:''' seconds, days, seasons
|-
| '''Units:''' gene expression, e.g. TPM
|-
| '''Community captured:''' size-fractioned, e.g. 0.2 - 250 µm, cultured or target species
|-
| '''Co-measurements:''' Other measurements required for interpretation of results e.g., temperature, salinity, nutrients, physiological data
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

== Output ==

=== Scale of measurement ===

=== Data generated ===

=== Units & currency ===

=== Sample size ===

=== Repositories & databases ===

== Limitations ==

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

=== Common calculations/conversions ===
* Normalised expression, for example transcripts per million (TPM)
* Quantitative estimates, for example transcripts per L (TPL)

== References ==

[[Category:Main Pages|Model types]]